5vr9

CH1/Ckappa Fab based on Matuzumab

Method: X-RAY DIFFRACTION D_max: 98.4 Å Quality: EXCELLENT

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

CH1/Ckappa Fab heavy chain

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 122–238	Not recorded	CH1/Ckappa Fab light chain × 1 （Q7Z3Y4）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；294 K；see publication for details	Resolution 2.15 Å R-free 0.244
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 122–238	Not recorded	CH1/Ckappa Fab light chain × 1 （Q7Z3Y4）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；294 K；see publication for details	Resolution 2.15 Å R-free 0.244

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5VR9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ZA6 The structure of an antitumor CH2-domain-deleted humanized antibody Deposited 2005-04-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 225–465（241 aa） Chain D 225–465（241 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；290 K；4 M sodium formate, 1.5 mM Triton X-100 detergent, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20	Resolution 2.80 Å R-free 0.296
1ZA6 The structure of an antitumor CH2-domain-deleted humanized antibody Deposited 2005-04-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 225–465（241 aa） Chain H 225–465（241 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；290 K；4 M sodium formate, 1.5 mM Triton X-100 detergent, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20	Resolution 2.80 Å R-free 0.296
1ZA6 The structure of an antitumor CH2-domain-deleted humanized antibody Deposited 2005-04-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain B 225–465（241 aa） Chain D 225–465（241 aa） Chain F 225–465（241 aa） Chain H 225–465（241 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；290 K；4 M sodium formate, 1.5 mM Triton X-100 detergent, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20	Resolution 2.80 Å R-free 0.296
1ZA6 The structure of an antitumor CH2-domain-deleted humanized antibody Deposited 2005-04-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 225–465（241 aa） Chain D 225–465（241 aa） Chain F 225–465（241 aa） Chain H 225–465（241 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；290 K；4 M sodium formate, 1.5 mM Triton X-100 detergent, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20	Resolution 2.80 Å R-free 0.296
4D9L Fab structure of anti-HIV-1 gp120 V2 mAb 697 Deposited 2012-01-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 131–237（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；18% polyethylene glycol 8000 and 0.1 M Tris pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.48 Å R-free 0.238
4D9L Fab structure of anti-HIV-1 gp120 V2 mAb 697 Deposited 2012-01-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 131–237（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；18% polyethylene glycol 8000 and 0.1 M Tris pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.48 Å R-free 0.238
4D9L Fab structure of anti-HIV-1 gp120 V2 mAb 697 Deposited 2012-01-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 131–237（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；18% polyethylene glycol 8000 and 0.1 M Tris pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.48 Å R-free 0.238
4D9L Fab structure of anti-HIV-1 gp120 V2 mAb 697 Deposited 2012-01-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 131–237（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；18% polyethylene glycol 8000 and 0.1 M Tris pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.48 Å R-free 0.238
5O1R human Fab 5H2 bound to NHBA-C3 from Neisseria meningitidis serogroup B Deposited 2017-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 20–240（221 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M TRIS pH 8.0 and 1.6 M lithium sulphate	Resolution 2.86 Å R-free 0.222
5O1R human Fab 5H2 bound to NHBA-C3 from Neisseria meningitidis serogroup B Deposited 2017-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 20–240（221 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M TRIS pH 8.0 and 1.6 M lithium sulphate	Resolution 2.86 Å R-free 0.222
5UTZ Human IL-2/Fab complex Deposited 2017-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 128–238（111 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；100 mM sodium citrate, pH 5.0, 20% PEG6000	Resolution 2.75 Å R-free 0.247
5UTZ Human IL-2/Fab complex Deposited 2017-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 128–238（111 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；100 mM sodium citrate, pH 5.0, 20% PEG6000	Resolution 2.75 Å R-free 0.247
5UTZ Human IL-2/Fab complex Deposited 2017-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 128–238（111 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；100 mM sodium citrate, pH 5.0, 20% PEG6000	Resolution 2.75 Å R-free 0.247
5UTZ Human IL-2/Fab complex Deposited 2017-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 128–238（111 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；100 mM sodium citrate, pH 5.0, 20% PEG6000	Resolution 2.75 Å R-free 0.247
5VSI CH1/Ckappa Fab mutant 15.1 Deposited 2017-05-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 122–235（114 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 5 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；294 K；see publication	Resolution 1.51 Å R-free 0.227
6AL4 CRYSTAL STRUCTURE OF ANTI-CD19 ANTIBODY B43 FAB Deposited 2017-08-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 125–238（114 aa） Fragment：FD,FD,FD,FD	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.1；293 K；20% PEG 3350, 0.2 M NA PHOSPHATE DIBASIC	Resolution 2.45 Å R-free 0.236
6AL4 CRYSTAL STRUCTURE OF ANTI-CD19 ANTIBODY B43 FAB Deposited 2017-08-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 125–238（114 aa） Fragment：FD,FD,FD,FD	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.1；293 K；20% PEG 3350, 0.2 M NA PHOSPHATE DIBASIC	Resolution 2.45 Å R-free 0.236
6AL4 CRYSTAL STRUCTURE OF ANTI-CD19 ANTIBODY B43 FAB Deposited 2017-08-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 125–238（114 aa） Fragment：FD,FD,FD,FD	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.1；293 K；20% PEG 3350, 0.2 M NA PHOSPHATE DIBASIC	Resolution 2.45 Å R-free 0.236
6APD Crystal structure of RSV F bound by AM22 and the infant antibody ADI-19425 Deposited 2017-08-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain D 123–239（117 aa） Chain F 123–239（117 aa） Chain H 123–239（117 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；10% PEG 4000 10% 2-propanol 0.1 M sodium citrate pH 5.5	Resolution 4.10 Å R-free 0.256
6B9Y Trastuzumab Fab v3 in complex with 5-phenyl meditope variant Deposited 2017-10-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 124–238（115 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.5, 15% PEG3350, 24 mM NaCl	Resolution 2.14 Å R-free 0.218
6BAH Trastuzumab Fab v3 with 5-diphenyl meditope variant Deposited 2017-10-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 124–238（115 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris, pH 7.5, 24 mM NaCl, 15% PEG 3350	Resolution 1.90 Å R-free 0.194
6DC4 RSV-neutralizing human antibody AM22 Deposited 2018-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 123–239（117 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 17	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.02 M 1,6-Hexanediol, 0.02 M 1-Butanol, 0.02 M 1,2-Propanediol (racemic), 0.02 M 2-Propanol, 0.02 M 1,4-Butanediol, 0.02 M 1,3-Propanediol, 0.1 M MES/imidazole pH 6.5, 10% PEG 8000, 20% ethylene glycol	Resolution 1.70 Å R-free 0.205
6DC5 RSV prefusion F in complex with AM22 Fab Deposited 2018-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 123–239（117 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CD CADMIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；32% PEG 400, 4% PEG 3350, 0.01 M cadmium chloride, 0.1 M sodium acetate pH 5.5	Resolution 3.50 Å R-free 0.280
6DC5 RSV prefusion F in complex with AM22 Fab Deposited 2018-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 123–239（117 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CD CADMIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；32% PEG 400, 4% PEG 3350, 0.01 M cadmium chloride, 0.1 M sodium acetate pH 5.5	Resolution 3.50 Å R-free 0.280
6DC5 RSV prefusion F in complex with AM22 Fab Deposited 2018-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 123–239（117 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CD CADMIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；32% PEG 400, 4% PEG 3350, 0.01 M cadmium chloride, 0.1 M sodium acetate pH 5.5	Resolution 3.50 Å R-free 0.280
6OGE Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab complex Deposited 2019-04-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 124–235（112 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.36 Å
6VPY I33M (I3.2 mutant from CH103 Lineage) Deposited 2020-02-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 125–240（116 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.5 M ammonium sulfate, 100 mM HEPES, pH 7.23, 5% PEG400	Resolution 2.36 Å R-free 0.223
6VPY I33M (I3.2 mutant from CH103 Lineage) Deposited 2020-02-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 125–240（116 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.5 M ammonium sulfate, 100 mM HEPES, pH 7.23, 5% PEG400	Resolution 2.36 Å R-free 0.223
7CZR S protein of SARS-CoV-2 in complex bound with P5A-1B8_2B Deposited 2020-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 123–465（343 aa） Chain J 123–465（343 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7CZS S protein of SARS-CoV-2 in complex bound with P5A-1B8_3B Deposited 2020-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain H 123–465（343 aa） Chain I 123–465（343 aa） Chain J 123–465（343 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7CZX S protein of SARS-CoV-2 in complex bound with P5A-1B9 Deposited 2020-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain H 121–465（345 aa） Chain I 121–465（345 aa） Chain J 121–465（345 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7D00 S protein of SARS-CoV-2 in complex bound with FabP5A-1B8 Deposited 2020-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 123–465（343 aa） Chain J 123–465（343 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8BBO SARS-CoV-2 Delta-RBD complexed with BA.2-36 Fab Deposited 2022-10-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 20–240（221 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；2% (v/v) PEG400, 0.1M imidazole pH7.0 and 24% (w/v) PEG MME 5000.	Resolution 2.75 Å R-free 0.252

18 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6GMX6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 108–224； UniProt 122–238 Author chain H； PDBConstruct 108–224； UniProt 122–238

CH1/Ckappa Fab light chain

Homo sapiens

UniProt Q7Z3Y4

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 130–235	Not recorded	CH1/Ckappa Fab heavy chain × 1 （Q6GMX6）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；294 K；see publication for details	Resolution 2.15 Å R-free 0.244
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain L； UniProt 130–235	Not recorded	CH1/Ckappa Fab heavy chain × 1 （Q6GMX6）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；294 K；see publication for details	Resolution 2.15 Å R-free 0.244

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5VR9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1L7I Crystal Structure of the anti-ErbB2 Fab2C4 Deposited 2002-03-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 23–236（214 aa） Fragment：light chain (residues 1-214)	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；35%-45% saturated (NH4)2SO4, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.80 Å R-free 0.230
5VL7 PCSK9 complex with Fab33 Deposited 2017-04-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 127–236（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；potassium sodium phosphate	Resolution 3.50 Å R-free 0.245
5VSI CH1/Ckappa Fab mutant 15.1 Deposited 2017-05-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 130–235（106 aa）	Not recorded	SO4 SULFATE ION × 5 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；294 K；see publication	Resolution 1.51 Å R-free 0.227
6BGT Structure of Trastuzumab Fab mutant in complex with Her2 extracellular domain Deposited 2017-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 127–236（110 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；100 mM MES, pH 6.5, 18% PEG3350, 10% glycerol	Resolution 2.70 Å R-free 0.247
6MH2 Structure of Herceptin Fab without antigen Deposited 2018-09-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 127–236（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；200 mM ammonium acetate, 100 mM Bis-Tris, pH 5.5, 25% v/v PEG3350	Resolution 2.80 Å R-free 0.306
6MH2 Structure of Herceptin Fab without antigen Deposited 2018-09-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 127–236（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；200 mM ammonium acetate, 100 mM Bis-Tris, pH 5.5, 25% v/v PEG3350	Resolution 2.80 Å R-free 0.306
6MXR Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M] Deposited 2018-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 127–236（110 aa） Chain L 127–236（110 aa）	Not recorded	CL CHLORIDE ION × 2 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 5.6；295 K；0.1 M tris-sodium citrate, pH 5.6, 11% PEG4000, 8% isopropanol	Resolution 2.04 Å R-free 0.200
6MXS Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M] Deposited 2018-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 127–236（110 aa） Chain L 127–236（110 aa）	Not recorded	CL CHLORIDE ION × 2 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 5.6；295 K；0.1 M tri-sodium citrate, pH 5.6, 12% PEG4000, 10% isopropanol	Resolution 1.95 Å R-free 0.229
6MY4 Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M,LC-S30bR] Deposited 2018-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 127–236（110 aa） Chain L 127–236（110 aa）	Mutation：S30bR,S30bR Mutation：S30bR,S30bR	EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8；295 K；0.05 M imidazole, pH 8.0, 18% PEG6000	Resolution 1.69 Å R-free 0.230
6MY5 Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M,LC-S30bR] Deposited 2018-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 127–236（110 aa） Chain L 127–236（110 aa）	Mutation：S30bR,S30bR Mutation：S30bR,S30bR	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8；295 K；0.04 M imidazole, pH 8.0, 21% PEG6000	Resolution 1.73 Å R-free 0.229
6U1N GPCR-Beta arrestin structure in lipid bilayer Deposited 2019-08-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 127–236（110 aa）	Not recorded	2CU 3-amino-5-chloro-N-cyclopropyl-4-methyl-6-[2-(4-methylpiperazin-1-yl)-2-oxoethoxy]thieno[2,3-b]pyridine-2-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7ZLG Cryo-EM structure of C-mannosyltransferase CeDPY19, in complex with acceptor peptide and bound to CMT2-Fab and anti-Fab nanobody Deposited 2022-04-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain L 23–236（214 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.72 Å
7ZLI Cryo-EM structure of C-mannosyltransferase CeDPY19, in complex with Dol25-P-Man and bound to CMT2-Fab and anti-Fab nanobody Deposited 2022-04-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 23–236（214 aa）	Not recorded	IZY Dolichol monophosphate beta-D-Mannose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.99 Å
7ZLJ Cryo-EM structure of C-mannosyltransferase CeDPY19, in ternary complex with Dol25-P-C-Man and acceptor peptide, bound to CMT2-Fab and anti-Fab nanobody Deposited 2022-04-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain L 23–236（214 aa）	Not recorded	IZU [(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl-[(3~{S},6~{E},10~{Z},14~{E})-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenoxy]phosphinic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.63 Å
9BDG Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85647 Deposited 2024-04-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric	Chain G 23–236（214 aa） Chain H 23–236（214 aa） Chain I 23–236（214 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9MY8 D7 Herpes Virus Simplex Neutralizing Nanobody Bound to HSV Glycoprotein gD Deposited 2025-01-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 23–236（214 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.30 Å

15 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q7Z3Y4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 107–212； UniProt 130–235 Author chain L； PDBConstruct 107–212； UniProt 130–235

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5vr9
Deposition date deposition_date	2017-05-10
Structure title title	CH1/Ckappa Fab based on Matuzumab
Keywords keywords	bispecific antibody, computational design, heavy chain/light chain interface, CH1/Ckappa interface, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	31.73 Å
Radius of gyration Rg (electron density) rg_electron	30.70 Å
Forward intensity I(0) i0	140573000.00
Molecular weight molecular_weight	91684.0 kDa
Excluded volume excluded_volume	113600 Å³
Envelope volume envelope_volume	151240 Å³
Hydration-shell volume shell_volume	40939 Å³
Envelope diameter envelope_diameter	102.5 Å
Shell Rg shell_rg	38.28 Å
Envelope Rg envelope_rg	30.18 Å
Shape Rg shape_rg	30.71 Å
Total Rg total_rg	31.35 Å
Total atoms total_atoms	6462
Residues n_residues	868
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	98.4 Å
Rg (real space) rg_real	31.58 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	1.4060e+08
I(0) uncertainty (real space) i0_real_error	2.0000e+06
Rg (reciprocal space) rg_reciprocal	31.65 Å
I(0) (reciprocal space) i0_reciprocal	140600000.0000
Solution quality estimate total_estimate	0.9107
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.3 Å
Skewness Skewness skewness	0.136
Kurtosis Kurtosis kurtosis	-0.582
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21550000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.966

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CH1/Ckappa Fab heavy chain
Molecular weight formula_weight	24190.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,H
Atom count atom_count	6868

QVQLVQSGAEVKKPGASVKVSCKASGYTFTSHWMHWVRQAPGQGLEWIGEFNPSNGRTNYNEKFKSKATMTVDTSTNTAYMELSSLRSEDTAVYYCASRDYDYDGRYFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	CH1/Ckappa Fab light chain
Molecular weight formula_weight	23235.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,L

DIQMTQSPSSLSASVGDRVTITCSASSSVTYMYWYQQKPGKAPKLLIYDTSNLASGVPSRFSGSGSGTDYTFTISSLQPEDIATYYCQQWSSHIFTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	365

▼

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5vr9b1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d5vr9b2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d5vr9l1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d5vr9l2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (6 domains)

Domain ID domain_id	5vr9A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vr9B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vr9B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vr9H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vr9L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vr9L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	152.046 Å
Unit-cell length b length_b	152.046 Å
Unit-cell length c length_c	220.619 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2116
R_work r_work	0.2098
R_free r_free	0.2439

fit	/app/data/saxs_computation/vr/5vr9/5vr9.fit
pddf	/app/data/pr_computation/vr/5vr9/5vr9.pr.out
profile	/app/data/saxs_computation/vr/5vr9/5vr9.dat

CH1/Ckappa Fab based on Matuzumab

1. Protein Identity and Related Structures Protein Identity & Related Structures

CH1/Ckappa Fab heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

CH1/Ckappa Fab light chain

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)